Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast

A I Garrido-Godino; I Gupta; F Gutiérrez-Santiago; A B Martínez-Padilla; A Alekseenko; L M Steinmetz; J E Pérez-Ortín; V Pelechano; F Navarro

doi:10.1080/15476286.2020.1839229

Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast

RNA Biol. 2021 Aug;18(8):1206-1220. doi: 10.1080/15476286.2020.1839229. Epub 2020 Nov 1.

Authors

A I Garrido-Godino¹, I Gupta², F Gutiérrez-Santiago¹, A B Martínez-Padilla¹, A Alekseenko³, L M Steinmetz^{4

5

6}, J E Pérez-Ortín⁷, V Pelechano³, F Navarro^{1

8}

Affiliations

¹ Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain.
² Department of Biochemical Engineering and Biotechnology, IIT Delhi, Hauz Khas, India.
³ SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
⁴ European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
⁵ Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.
⁶ Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA.
⁷ E.R.I. Biotecmed, Facultad de Biológicas, Universitat de València, Burjassot, Spain.
⁸ Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain.

Abstract

Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analysed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.

Keywords: Puf3; RNA polymerase II; Rbp; Saccharomyces cerevisiae; mRNA decay; mRNA imprinting.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Binding Sites
Chromatin / chemistry
Chromatin / metabolism
Gene Expression Regulation, Fungal
Genomic Imprinting*
Molecular Sequence Annotation
Protein Binding
RNA Polymerase II / genetics*
RNA Polymerase II / metabolism
RNA Processing, Post-Transcriptional*
RNA Stability
RNA, Messenger / classification
RNA, Messenger / genetics*
RNA, Messenger / metabolism
RNA-Binding Proteins / genetics*
RNA-Binding Proteins / metabolism
Saccharomyces cerevisiae / genetics*
Saccharomyces cerevisiae / metabolism
Saccharomyces cerevisiae Proteins / genetics*
Saccharomyces cerevisiae Proteins / metabolism
Transcription, Genetic

Substances

Chromatin
PUF3 protein, S cerevisiae
RNA, Messenger
RNA-Binding Proteins
Saccharomyces cerevisiae Proteins
RNA Polymerase II
RPB4 protein, S cerevisiae

Grants and funding

This work has been supported by grants from the Spanish Ministry of Economy and Competitiveness (MINECO) and ERDF (BFU2016-77728-C3-2-P to F.N. and BFU2016-77728-C3-3-P to J.E.P-O), Spanish Ministry of Science and Innovation (MICINN) and ERDF (RED2018-102467-T to F. N. and J.E.P-O), the Junta de Andalucía (BIO258 to F. N.), Junta de Andalucía-Universidad de Jaén (FEDER-UJA 1260360 to F.N.), the Generalitat Valenciana (AICO/2019/088 to J.E.P-O) and DFG grant (STE 1422/4-1) to L.M.S. VP’s laboratory is funded by the Swedish Research Council (VR 2016-01842), a Wallenberg Academy Fellowship (KAW 2016.0123), the Swedish Foundations’ Starting Grant (Ragnar Söderberg Foundation), Karolinska Institutet (SciLifeLab Fellowship, SFO, KID and KI funds). IG is funded by a Seed funding grant provided by the Indian Institute of Technology, Delhi. A.I.G-G was financed by the University of Jaen, MINECO and ERDF funds (BFU2016-77728-C3-2-P to F.N.). F.G-S. is a recipient of a predoctoral fellowship from the Universidad de Jaén.